KSM outperforms PWM in predicting in vivo TF binding in held-out data. (A) The partial ROC performance of KSM, KMAC PWM, MEME PWM, and HOMER PWM for predicting ChIP-seq binding of GABP in K562 cells. (B) Scatter plot comparing the mean KSM scores of positive sequences and mean KSM scores of negative sequences that corresponds to the same PWM scores in the K562 GABP data set. Each point represents a set of sequences that have the same PWM score. (C) Scatter plot comparing the mean partial AUROC (FPR ≤ 0.1) values of KSM and PWM for predicting ChIP-seq binding for 104 experiments. (D) Similar to C, but comparing KSM and PWM in the same cell type (red) or across cell type (blue) in 19 TFs.
